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Hostname	OS	Arch (*)	R version	Installed pkgs
nebbiolo2	Linux (Ubuntu 24.04.3 LTS)	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4882
merida1	macOS 12.7.6 Monterey	x86_64	4.5.2 (2025-10-31) -- "[Not] Part in a Rumble"	4673
kjohnson1	macOS 13.7.5 Ventura	arm64	4.5.2 Patched (2025-11-04 r88984) -- "[Not] Part in a Rumble"	4607
taishan	Linux (openEuler 24.03 LTS)	aarch64	4.5.0 (2025-04-11) -- "How About a Twenty-Six"	4671
Click on any hostname to see more info about the system (e.g. compilers) () as reported by 'uname -p', except on Windows and Mac OS X*

BUILD BIN results for Biobase on kjohnson1

To the developers/maintainers of the Biobase package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/Biobase.git to reflect on this report. SeeTroubleshooting Build Report for more information.
- Use the followingRenviron settings to reproduce errors and warnings.
- If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. SeeRenviron.bioc for more information.

raw results

Summary

Package: Biobase

Version: 2.70.0

Command: rm -rf Biobase.buildbin-libdir && mkdir Biobase.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Biobase_2.70.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Biobase.buildbin-libdir

StartedAt: 2025-12-14 08:24:04 -0500 (Sun, 14 Dec 2025)

EndedAt: 2025-12-14 08:24:23 -0500 (Sun, 14 Dec 2025)

EllapsedTime: 18.8 seconds

RetCode: 0

Status: OK

PackageFile: Biobase_2.70.0.tgz

PackageFileSize: 2.512MiB

Command output

################################################################################################################################################################## Running command:######   rm -rf Biobase.buildbin-libdir && mkdir Biobase.buildbin-libdir && /Users/biocbuild/BBS/utils/build-universal.sh Biobase_2.70.0.tar.gz /Library/Frameworks/R.framework/Resources/bin/R Biobase.buildbin-libdir###############################################################################################################################################################>>>>>>> >>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=Biobase.buildbin-libdir Biobase_2.70.0.tar.gz'>>>>>>> * installing *source* package ‘Biobase’ ...** this is package ‘Biobase’ version ‘2.70.0’** using staged installation** libsusing C compiler: ‘Apple clang version 15.0.0 (clang-1500.0.40.1)’using SDK: ‘MacOSX11.3.1.sdk’clang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c Rinit.c -o Rinit.oclang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c envir.c -o envir.oclang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c matchpt.c -o matchpt.oclang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c rowMedians.c -o rowMedians.oclang -arch arm64 -std=gnu2x -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG   -I/opt/R/arm64/include    -fPIC  -falign-functions=64 -Wall -g -O2  -c sublist_extract.c -o sublist_extract.oclang -arch arm64 -std=gnu2x -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -L/Library/Frameworks/R.framework/Resources/lib -L/opt/R/arm64/lib -o Biobase.so Rinit.o envir.o matchpt.o rowMedians.o sublist_extract.o -F/Library/Frameworks/R.framework/.. -framework Rinstalling to /Users/biocbuild/bbs-3.22-bioc/meat/Biobase.buildbin-libdir/00LOCK-Biobase/00new/Biobase/libs** R** data** inst** byte-compile and prepare package for lazy loading** help*** installing help indices** building package indices** installing vignettes** testing if installed package can be loaded from temporary location** checking absolute paths in shared objects and dynamic libraries** testing if installed package can be loaded from final location** testing if installed package keeps a record of temporary installation path* DONE (Biobase)>>>>>>> >>>>>>> FIXING PATHS TO DYNAMIC LIBRARIES FOR Biobase.buildbin-libdir/Biobase/libs/Biobase.so>>>>>>> >>>>>>> Paths before fix:Biobase.buildbin-libdir/Biobase/libs/Biobase.so:Biobase.so (compatibility version 0.0.0, current version 0.0.0)/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.2)/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)>>>>>>> Fix with install_name_tool:install_name_tool -change "/usr/local/lib/libgcc_s.1.1.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgcc_s.1.1.dylib" "Biobase.buildbin-libdir/Biobase/libs/Biobase.so"install_name_tool -change "/usr/local/lib/libgfortran.5.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libgfortran.5.dylib" "Biobase.buildbin-libdir/Biobase/libs/Biobase.so"install_name_tool -change "/usr/local/lib/libquadmath.0.dylib" "/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libquadmath.0.dylib" "Biobase.buildbin-libdir/Biobase/libs/Biobase.so">>>>>>> Paths after fix:Biobase.buildbin-libdir/Biobase/libs/Biobase.so:Biobase.so (compatibility version 0.0.0, current version 0.0.0)/Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libR.dylib (compatibility version 4.5.0, current version 4.5.2)/usr/lib/libSystem.B.dylib (compatibility version 1.0.0, current version 1292.100.5)